comparison snippy.xml @ 6:15f5a3074012 draft

Added snippy core and static binaries for linux and mac.

5:ff31f16f5dfd

<tool id="snippy" name="snippy" version="0.2.0">
    <requirements>
      <requirement type="package" version="3.0">snippy</requirement>
      <requirement type="package" version="1.2">samtools</requirement>
      <requirement type="package" version="0_9_20_b040236">freebayes</requirement>
      <requirement type="package" version="0.7.12">bwa</requirement>
      <requirement type="package" version="0.1.11">vcftools</requirement>
      <requirement type="package" version="4.0">snpeff</requirement>
      <requirement type="package" version="8a5602bf07">vcflib</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>

    <command><![CDATA[
      #if str( $reftype.ref_type_selector ) == "fasta"
        cp $reftype.ref foo.fna &&
      #end if

      #end if

      &&

      gunzip out/snps.depth.gz


    ]]></command>
    <inputs>
      <conditional name="reftype">

      <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa"/>
      <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth"/>
      <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
        <filter>cleanup is False</filter>
      </data>
    </outputs>

    <tests>
      <test>
        <param name="ref_type_selector" value="fasta" />

  --rgid [X]        Use this @RG ID: in the BAM header (default '')

  --bwaopt [X]      Extra BWA MEM options, eg. -x pacbio (default '')

    ]]></help>

    <citations>
      <citation type="bibtex">@UNPUBLISHED{Seemann2013,
        author = "Seemann T",
        title = "snippy: fast bacterial variant calling from NGS reads",
        year = "2015",
        note = "https://github.com/tseemann/snippy"}
      </citation>
    </citations>

</tool>

6:15f5a3074012

<tool id="snippy" name="snippy" version="0.2.0">
  <requirements>
      <requirement type="package" version="3.0">snippy</requirement>
  </requirements>
  <stdio>
      <exit_code range="1:" />
  </stdio>

    <command><![CDATA[
      #if str( $reftype.ref_type_selector ) == "fasta"
        cp $reftype.ref foo.fna &&
      #end if

      #end if

      &&

      gunzip out/snps.depth.gz

      &&

      tar -czf out.tgz out


    ]]></command>
    <inputs>
      <conditional name="reftype">

      <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa"/>
      <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth"/>
      <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
        <filter>cleanup is False</filter>
      </data>
      <data format="zip" name="outdir" label="${tool.name} on ${on_string} out dir" from_work_dir="out.tgz" />
    </outputs>

    <tests>
      <test>
        <param name="ref_type_selector" value="fasta" />

  --rgid [X]        Use this @RG ID: in the BAM header (default '')

  --bwaopt [X]      Extra BWA MEM options, eg. -x pacbio (default '')

    ]]></help>
  <citations>
    <citation type="bibtex">@UNPUBLISHED{Seemann2013,
      author = "Seemann T",
      title = "snippy: fast bacterial variant calling from NGS reads",
      year = "2015",
      note = "https://github.com/tseemann/snippy"}</citation>
  </citations>


</tool>